Hello, There seems to be a problem in retrieving annotation from the chip "affy_huex_1_0_st_v2". >library(biomaRt) >ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok #check if "affy_huex_1_0_st_v2" is a valid attribute >attributes=listAttributes(ensembl) >grep("affy_huex_1_0_st_v2",attributes[,1]) [1] 13 #collect data >data=getBM(attributes="affy_huex_1_0_st_v2", mart=ensembl) Error in postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery) : transfer closed with outstanding read data remaining > sessionInfo() R version 2.8.1 (2008-12-22) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] biomaRt_1.16.0 R.utils_1.1.1 R.oo_1.4.6 R.methodsS3_1.0.3 [5] Biobase_2.2.2 loaded via a namespace (and not attached): [1] RCurl_0.94-1 XML_2.3-0 Thank you for your help, Nenad Nenad Bartonicek European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom tel: +44-755-435-9057 [[alternative HTML version deleted]]

Hi Nenad, Nenad Bartonicek wrote: > Hello, > > There seems to be a problem in retrieving annotation from the chip > "affy_huex_1_0_st_v2". > > >library(biomaRt) > >ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl") > > Checking attributes and filters ... ok > > #check if "affy_huex_1_0_st_v2" is a valid attribute > >attributes=listAttributes(ensembl) > >grep("affy_huex_1_0_st_v2",attributes[,1]) > > [1] 13 > > #collect data > >data=getBM(attributes="affy_huex_1_0_st_v2", mart=ensembl) You are not asking for any data here. Do you get the same result if you include some values for the filter and values arguments? Best, Jim > > Error in postForm(paste(martHost(mart), "?", sep = ""), query = > xmlQuery) : > transfer closed with outstanding read data remaining > > > sessionInfo() > R version 2.8.1 (2008-12-22) > i386-apple-darwin8.11.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices datasets tools utils methods > [8] base > > other attached packages: > [1] biomaRt_1.16.0 R.utils_1.1.1 R.oo_1.4.6 > R.methodsS3_1.0.3 > [5] Biobase_2.2.2 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-1 XML_2.3-0 > > Thank you for your help, > > Nenad > > Nenad Bartonicek > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton > Cambridge > CB10 1SD > United Kingdom > tel: +44-755-435-9057 > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826